First I just want to say, I LOVE the name Aphrodite and I think it's fantastic that you were bold enough to use it.

Anyways, I think another bold choice is the best route to go, something that really pops. From your list my favorites with Aphrodite are...

Cleopatra... Love the historical reference and love that it is also very boldSerafina... Stunning name, it also has a nice history behind it

Other suggestions

Atlantis... I think this could be a really pretty choice and it has a cool mythological reference without being GreekCalypso... Also Greek, another strong female character, heroes often washed up on her shore and she nursed them, although sometimes it is said that she held them as prisoners to keep her company on her lonely island of Ogygia. Calliope... Another Greek choice, she was one of the nine muses, she bore many children in mythology including Orpheus

I absolutely love Hermione--it was on my list for a while! I think Hermione and Aphrodite go well together. There is the HarryPotter thing which other people have brought up. Personally, I'm a huge HarryPotter fan and wouldn't feel comfortable naming my child a "HarryPotter name" because of that--I know my friends/relatives would leap to conclusions and think I'd gone overboard in my fangirling. However, if you're surrounded by people who wouldn't judge or if you don't care about the association, I think Hermione's the best fit!